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MHC class II typing

mhcflow implements the polysolver algorithm and further extends its application to genotyping class II MHC alleles. Pre-built resources for class II typing are provided in the reference/class2/ folder of the repository:

reference
├─ class2/
│  ├─ class2.ref.fasta
│  ├─ class2.ref.38mer.tag
│  ├─ class2.ref.supertype.freq.tsv
│  └─ class2.chr_prefix_free.bed
  • class2.ref.fasta: The class II HLA reference used with --hla_ref option.
  • class2.ref.38mer.tag: The Kmer sequences generated from the class II reference, provided to --tag option.
  • class2.ref.supertype.freq.tsv: The population frequency of class II alleles at 4-digit resolution, provided to --freq option.
  • class2.chr_prefix_free.bed: A BED file that specifies the regions of class II genes. The coordinates in this file are based on the hg19 genome build.

Note

If you intent to type a specific set of class II alleles, simply replace these file according to the instruction in Build custom MHC reference.

Note

mhcflow does not provide accompanying .fai and .nix files along with the Fasta file. Please generate them using samtools faidx and novoindex prior to running mhcflow.

Note

The class II BED file uses 6 as chromosome 6. If your genome reference employs a different naming scheme, please update the file accordingly.

Genotyping class II alleles

Swapping in the class II resources for the mhcflow command demonstrated in Getting Started guide to genotype class II alleles:

mhcflow --bam [Genomic alignment] \
  --hla_ref class2.ref.fasta \
  --bed class2.chr_prefix_free.bed \
  --tag class2.ref.38mer.tag \
  --freq class2.ref.supertype.freq.tsv \
  --outdir [Path ot output folder]

Benchmark

A preliminary benchmark for class II typing was performed using samples from 1000 Genome project. The results were suprisingly promising and are available here.

Note

The class II benchmark was performed using the v0.1.0 branch of the mhcflow repository. I am still in the process of testing mhcflow on a subset of those samples.

Build custom MHC reference

Coming soon...